According to the Merriam-Webster Dictionary, the term in extremis means in extreme circumstances; especially: at the point of death. After the horror and jeopardy of “Oxygen” last week, what does that mean for Doctor Who? It cannot mean the Doctor, can it? Given a fifty year history of the Doctor’s survival, that seems highly unlikely.

No, what we get with this week’s episode, “Extremis,” is part Dan Brown and part the Wachowskis as something new menaces Earth. We also learn a lot about the mysterious vault, and this season’s long story arc. Our twelve episode journey for the year is now half over. Let’s see what it is all about.

It starts with one of the most annoying literary traditions about the Roman Catholic Church: the Church as the keeper of occult wisdom. It’s a frequent motif, with the author Dan Brown being only one of the most recent exponents. You can look at films like Prince of Darkness or End of Days. If you want to be apocryphal and discuss long hidden secrets, lost gospels, or the coming of the end times, Western literary tradition always turns toward Rome. There is always a library, a church, or a hidden religious order. It’s a secret handed down from Pope to Pope, or a book that not even the Pope knows about. I guess that’s what happens when there are centuries when you are about the only organization in Europe that cares about books and glues society together; you get stuck with being the ones who hang on to all sorts of dark secrets.

From there, we pretty quickly jump from old magic to new magic: quantum physics and cosmology. We go from the old temple (the Vatican) in Rome to the new one (CERN) in Switzerland. Physicists are the modern mystics, the modern alchemists. Here, science learns the dark secret at the heart of reality that religion has kept and is equally scared. What is at the heart of the new magic? Quantum mechanics is all about probabilities; it does not say exactly what is, but what could be at a given point in time. The science of the very small says that the universe is on some level random. Cosmology tells a different story; it is one of gravity, singularities, and event horizons. Here, reality is merely information. What we experience could be intrinsically real, or it could be just a hologram on the event horizon at the edge of the expanding universe created by the Big Bang. That is the gospel of the science of the very large. This episode of Doctor Who says that both fail us.

Finally, there is Missy. We learn that she is tied up with the themes of this season. That makes sense, and returns us to a theme from the Pertwee years of the early 1970s. The Doctor was trapped on Earth and needed a recurring enemy, an equal and opposite counterpart, to keep things from becoming just another story of Earthly invasion by aliens from week to week. Back then, it was Gallifrey keeping the Doctor trapped on Earth with the Master. Now, we discover that the Doctor is trapping himself on Earth for Missy.

Does it all work? I think it does not. It rings hollow in a few too many places. The re-introduction of the Master to Doctor Who in 2007 was about creating an adversary that was someone the Doctor loved and loathed at the same time. The Master was intrinsically that person; the history of the series told us that he was the Doctor’s equivalent opposite in all things. He also became the only other Time Lord in existence, and the only real tie to the Doctor’s past. The Doctor was nearly destroyed by what he did (or thought he did) during the Time War, and the Master was all those complex feelings in one person that he would have to destroy again.

Missy is none of those things. The Time Lords are back, though we haven’t heard from them lately. The Doctor isn’t alone. The connection between the Doctor and Missy is somehow more personal, but it is, at this point, less immediately accessible. It’s almost as if she’s the anti-River Song, but we don’t know the whole story. We can’t know it, really. Part of the Doctor’s power is in his mystery, and giving him a concrete history is always dangerous. No, we see the Doctor sacrifice for Missy, but we don’t have a good reason why. That robs the moment of much of its power.

As for the rest of the technobabble, it also rings a bit false. Not being truly random does not mean that the numbers you pull out of a hat are always the same. Simulations are instructive examples, but always contain much less information, much less nuance than the real thing. Yes, lowly little computer program subroutines can send e-mail, but only if they have permission. It doesn’t hang together too well.

No, Steven Moffat plays with some interesting themes for this week’s Doctor Who and offers some dramatic possibilities. We see the Doctor and Bill spar over the boundaries in her life. We see Peter Capaldi struggle with being the first Doctor to pay a serious personal price for his adventures. We see Matt Lucas finally given something that pulls Nardole into the story instead of pulling the Doctor and Bill back to Earth. That’s all well and good, but it sits on a framework that’s a little too much worn cliche for me.